0.019372
0.000000
-0.002999
0.000000
0.016300
0.000000
0.000000
0.000000
0.017139
0.00000
0.00000
0.00000
Prabu-Jeyabalan, M.
Nalivaika, E.A.
King, N.M.
Schiffer, C.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
81.20
90.00
51.620
61.350
59.040
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C37 H48 N6 O5 S2
720.944
RITONAVIR
A-84538
peptide-like
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
Y
290
N
C
Y
291
N
C
Y
292
N
S
Y
293
N
C
Y
294
N
N
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
N
N
300
S
C
N
301
S
C
N
302
N
C
N
303
S
C
N
304
N
C
Y
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
N
311
N
O
N
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
Y
318
N
C
N
319
N
N
N
320
N
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
C
N
326
N
C
N
327
N
C
N
328
N
N
N
329
N
C
N
330
N
O
Y
331
N
C
Y
332
N
C
Y
333
N
S
Y
334
N
C
Y
335
N
N
N
336
N
C
N
337
N
C
N
338
N
C
N
339
N
C
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
N
N
389
S
C
N
390
N
C
N
391
N
O
N
392
R
C
N
393
N
O
N
394
N
C
N
395
N
O
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
N
N
406
S
C
N
407
N
C
N
408
N
O
N
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
Y
413
N
N
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
N
419
N
O
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
N
443
N
O
N
444
N
O
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
N
N
457
S
C
N
458
N
C
N
459
N
O
N
460
N
C
N
461
N
C
N
462
N
C
N
463
N
O
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
Y
277
N
doub
Y
278
N
sing
N
279
N
sing
Y
280
N
sing
N
281
N
sing
Y
282
N
sing
Y
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
doub
N
315
N
sing
N
316
N
sing
N
317
N
sing
Y
318
N
doub
Y
319
N
sing
Y
320
N
sing
N
321
N
sing
Y
322
N
doub
N
323
N
sing
Y
324
N
sing
N
325
N
sing
Y
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
sing
N
340
N
sing
Y
341
N
doub
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
Y
359
N
doub
Y
360
N
sing
Y
361
N
sing
N
362
N
sing
Y
363
N
sing
Y
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
doub
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
doub
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
Y
405
N
doub
Y
406
N
sing
Y
407
N
sing
N
408
N
sing
Y
409
N
doub
Y
410
N
sing
Y
411
N
sing
N
412
N
sing
Y
413
N
sing
Y
414
N
doub
N
415
N
sing
Y
416
N
doub
N
417
N
sing
Y
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
doub
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
Y
433
N
doub
Y
434
N
sing
Y
435
N
sing
N
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
439
N
doub
N
440
N
sing
Y
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
doub
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
US
J.VIROL.
JOVIAM
0825
0022-538X
77
1306
1315
10.1128/JVI.77.2.1306-1315.2003
12502847
Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant:
Structural Insights for Better Antiviral Therapy
2003
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
301
1207
1220
10.1006/jmbi.2000.4018
How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease
2000
UK
Structure
STRUE6
2005
0969-2126
10
369
381
10.1016/S0969-2126(02)00720-7
Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes
2002
US
Protein Sci.
PRCIEI
0795
0961-8368
11
418
429
10.1110/ps.2520102
Lack of synergy for inhibitors targeting a multi-drug resistant HIV-1 protease
2002
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
92
2484
2488
ABT-538 Is a Potent Inhibitor of Human Immunodeficiency Virus Protease and has High Oral Bioavailability in Humans
1995
10.2210/pdb1n49/pdb
pdb_00001n49
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
200
1
Yale Mirrors
IMAGE PLATE
2001-08-07
RIGAKU RAXIS IV
Yale Mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
10772.724
Protease
3.4.23.16
Q7K, D25N, V82A
4
man
polymer
720.944
RITONAVIR
2
syn
non-polymer
18.015
water
28
nat
water
Retropepsin
no
no
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PANIIGRNLLTQIGCTLNF
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PANIIGRNLLTQIGCTLNF
A,B,C,D
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Lentivirus
Escherichia
sample
POL
11676
Human immunodeficiency virus 1
562
Escherichia coli
TAP106
PLASMID
pEN18
1
2.14
42.59
VAPOR DIFFUSION, HANGING DROP
6.2
sodium phosphate, sodium citrate, ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP
software
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Refinement description
Database references
Derived calculations
Data collection
Refinement description
1
0
2003-01-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2013-02-27
1
4
2017-10-11
1
5
2021-10-27
1
6
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Inactive wild-type HIV protease (D25N) complexed with its Gag substrate peptide, CA-p2
HIV-1 PROTEASE DIMER COMPLEXED WITH (RITONAVIR) A-84538
RCSB
Y
RCSB
2002-10-30
REL
RIT
RITONAVIR
HOH
water
1F7A
PDB
experimental model
Inhibitor
RITONAVIR
Peptide-like
RIT
301
2
RIT
RIT
301
B
RIT
401
2
RIT
RIT
401
D
HOH
3
3
HOH
HOH
100
A
HOH
10
3
HOH
HOH
101
A
HOH
11
3
HOH
HOH
102
A
HOH
12
3
HOH
HOH
103
A
HOH
41
3
HOH
HOH
104
A
HOH
47
3
HOH
HOH
105
A
HOH
50
3
HOH
HOH
106
A
HOH
1
3
HOH
HOH
302
B
HOH
2
3
HOH
HOH
303
B
HOH
8
3
HOH
HOH
304
B
HOH
13
3
HOH
HOH
305
B
HOH
15
3
HOH
HOH
306
B
HOH
16
3
HOH
HOH
307
B
HOH
37
3
HOH
HOH
308
B
HOH
38
3
HOH
HOH
309
B
HOH
48
3
HOH
HOH
310
B
HOH
14
3
HOH
HOH
100
C
HOH
21
3
HOH
HOH
101
C
HOH
49
3
HOH
HOH
102
C
HOH
54
3
HOH
HOH
103
C
HOH
4
3
HOH
HOH
402
D
HOH
5
3
HOH
HOH
403
D
HOH
7
3
HOH
HOH
404
D
HOH
23
3
HOH
HOH
405
D
HOH
24
3
HOH
HOH
406
D
HOH
30
3
HOH
HOH
407
D
HOH
32
3
HOH
HOH
408
D
HOH
59
3
HOH
HOH
409
D
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
ARG
14
n
14
ARG
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASN
25
n
25
ASN
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
LYS
41
n
41
LYS
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
PRO
63
n
63
PRO
63
A
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
ALA
82
n
82
ALA
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
LYS
7
n
7
LYS
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
ARG
14
n
14
ARG
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASN
25
n
25
ASN
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
ASN
37
n
37
ASN
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
LYS
41
n
41
LYS
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
PRO
63
n
63
PRO
63
B
VAL
64
n
64
VAL
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
ALA
82
n
82
ALA
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
CYS
95
n
95
CYS
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
PRO
1
n
1
PRO
1
C
GLN
2
n
2
GLN
2
C
ILE
3
n
3
ILE
3
C
THR
4
n
4
THR
4
C
LEU
5
n
5
LEU
5
C
TRP
6
n
6
TRP
6
C
LYS
7
n
7
LYS
7
C
ARG
8
n
8
ARG
8
C
PRO
9
n
9
PRO
9
C
LEU
10
n
10
LEU
10
C
VAL
11
n
11
VAL
11
C
THR
12
n
12
THR
12
C
ILE
13
n
13
ILE
13
C
ARG
14
n
14
ARG
14
C
ILE
15
n
15
ILE
15
C
GLY
16
n
16
GLY
16
C
GLY
17
n
17
GLY
17
C
GLN
18
n
18
GLN
18
C
LEU
19
n
19
LEU
19
C
LYS
20
n
20
LYS
20
C
GLU
21
n
21
GLU
21
C
ALA
22
n
22
ALA
22
C
LEU
23
n
23
LEU
23
C
LEU
24
n
24
LEU
24
C
ASN
25
n
25
ASN
25
C
THR
26
n
26
THR
26
C
GLY
27
n
27
GLY
27
C
ALA
28
n
28
ALA
28
C
ASP
29
n
29
ASP
29
C
ASP
30
n
30
ASP
30
C
THR
31
n
31
THR
31
C
VAL
32
n
32
VAL
32
C
LEU
33
n
33
LEU
33
C
GLU
34
n
34
GLU
34
C
GLU
35
n
35
GLU
35
C
MET
36
n
36
MET
36
C
ASN
37
n
37
ASN
37
C
LEU
38
n
38
LEU
38
C
PRO
39
n
39
PRO
39
C
GLY
40
n
40
GLY
40
C
LYS
41
n
41
LYS
41
C
TRP
42
n
42
TRP
42
C
LYS
43
n
43
LYS
43
C
PRO
44
n
44
PRO
44
C
LYS
45
n
45
LYS
45
C
MET
46
n
46
MET
46
C
ILE
47
n
47
ILE
47
C
GLY
48
n
48
GLY
48
C
GLY
49
n
49
GLY
49
C
ILE
50
n
50
ILE
50
C
GLY
51
n
51
GLY
51
C
GLY
52
n
52
GLY
52
C
PHE
53
n
53
PHE
53
C
ILE
54
n
54
ILE
54
C
LYS
55
n
55
LYS
55
C
VAL
56
n
56
VAL
56
C
ARG
57
n
57
ARG
57
C
GLN
58
n
58
GLN
58
C
TYR
59
n
59
TYR
59
C
ASP
60
n
60
ASP
60
C
GLN
61
n
61
GLN
61
C
ILE
62
n
62
ILE
62
C
PRO
63
n
63
PRO
63
C
VAL
64
n
64
VAL
64
C
GLU
65
n
65
GLU
65
C
ILE
66
n
66
ILE
66
C
CYS
67
n
67
CYS
67
C
GLY
68
n
68
GLY
68
C
HIS
69
n
69
HIS
69
C
LYS
70
n
70
LYS
70
C
ALA
71
n
71
ALA
71
C
ILE
72
n
72
ILE
72
C
GLY
73
n
73
GLY
73
C
THR
74
n
74
THR
74
C
VAL
75
n
75
VAL
75
C
LEU
76
n
76
LEU
76
C
VAL
77
n
77
VAL
77
C
GLY
78
n
78
GLY
78
C
PRO
79
n
79
PRO
79
C
THR
80
n
80
THR
80
C
PRO
81
n
81
PRO
81
C
ALA
82
n
82
ALA
82
C
ASN
83
n
83
ASN
83
C
ILE
84
n
84
ILE
84
C
ILE
85
n
85
ILE
85
C
GLY
86
n
86
GLY
86
C
ARG
87
n
87
ARG
87
C
ASN
88
n
88
ASN
88
C
LEU
89
n
89
LEU
89
C
LEU
90
n
90
LEU
90
C
THR
91
n
91
THR
91
C
GLN
92
n
92
GLN
92
C
ILE
93
n
93
ILE
93
C
GLY
94
n
94
GLY
94
C
CYS
95
n
95
CYS
95
C
THR
96
n
96
THR
96
C
LEU
97
n
97
LEU
97
C
ASN
98
n
98
ASN
98
C
PHE
99
n
99
PHE
99
C
PRO
1
n
1
PRO
1
D
GLN
2
n
2
GLN
2
D
ILE
3
n
3
ILE
3
D
THR
4
n
4
THR
4
D
LEU
5
n
5
LEU
5
D
TRP
6
n
6
TRP
6
D
LYS
7
n
7
LYS
7
D
ARG
8
n
8
ARG
8
D
PRO
9
n
9
PRO
9
D
LEU
10
n
10
LEU
10
D
VAL
11
n
11
VAL
11
D
THR
12
n
12
THR
12
D
ILE
13
n
13
ILE
13
D
ARG
14
n
14
ARG
14
D
ILE
15
n
15
ILE
15
D
GLY
16
n
16
GLY
16
D
GLY
17
n
17
GLY
17
D
GLN
18
n
18
GLN
18
D
LEU
19
n
19
LEU
19
D
LYS
20
n
20
LYS
20
D
GLU
21
n
21
GLU
21
D
ALA
22
n
22
ALA
22
D
LEU
23
n
23
LEU
23
D
LEU
24
n
24
LEU
24
D
ASN
25
n
25
ASN
25
D
THR
26
n
26
THR
26
D
GLY
27
n
27
GLY
27
D
ALA
28
n
28
ALA
28
D
ASP
29
n
29
ASP
29
D
ASP
30
n
30
ASP
30
D
THR
31
n
31
THR
31
D
VAL
32
n
32
VAL
32
D
LEU
33
n
33
LEU
33
D
GLU
34
n
34
GLU
34
D
GLU
35
n
35
GLU
35
D
MET
36
n
36
MET
36
D
ASN
37
n
37
ASN
37
D
LEU
38
n
38
LEU
38
D
PRO
39
n
39
PRO
39
D
GLY
40
n
40
GLY
40
D
LYS
41
n
41
LYS
41
D
TRP
42
n
42
TRP
42
D
LYS
43
n
43
LYS
43
D
PRO
44
n
44
PRO
44
D
LYS
45
n
45
LYS
45
D
MET
46
n
46
MET
46
D
ILE
47
n
47
ILE
47
D
GLY
48
n
48
GLY
48
D
GLY
49
n
49
GLY
49
D
ILE
50
n
50
ILE
50
D
GLY
51
n
51
GLY
51
D
GLY
52
n
52
GLY
52
D
PHE
53
n
53
PHE
53
D
ILE
54
n
54
ILE
54
D
LYS
55
n
55
LYS
55
D
VAL
56
n
56
VAL
56
D
ARG
57
n
57
ARG
57
D
GLN
58
n
58
GLN
58
D
TYR
59
n
59
TYR
59
D
ASP
60
n
60
ASP
60
D
GLN
61
n
61
GLN
61
D
ILE
62
n
62
ILE
62
D
PRO
63
n
63
PRO
63
D
VAL
64
n
64
VAL
64
D
GLU
65
n
65
GLU
65
D
ILE
66
n
66
ILE
66
D
CYS
67
n
67
CYS
67
D
GLY
68
n
68
GLY
68
D
HIS
69
n
69
HIS
69
D
LYS
70
n
70
LYS
70
D
ALA
71
n
71
ALA
71
D
ILE
72
n
72
ILE
72
D
GLY
73
n
73
GLY
73
D
THR
74
n
74
THR
74
D
VAL
75
n
75
VAL
75
D
LEU
76
n
76
LEU
76
D
VAL
77
n
77
VAL
77
D
GLY
78
n
78
GLY
78
D
PRO
79
n
79
PRO
79
D
THR
80
n
80
THR
80
D
PRO
81
n
81
PRO
81
D
ALA
82
n
82
ALA
82
D
ASN
83
n
83
ASN
83
D
ILE
84
n
84
ILE
84
D
ILE
85
n
85
ILE
85
D
GLY
86
n
86
GLY
86
D
ARG
87
n
87
ARG
87
D
ASN
88
n
88
ASN
88
D
LEU
89
n
89
LEU
89
D
LEU
90
n
90
LEU
90
D
THR
91
n
91
THR
91
D
GLN
92
n
92
GLN
92
D
ILE
93
n
93
ILE
93
D
GLY
94
n
94
GLY
94
D
CYS
95
n
95
CYS
95
D
THR
96
n
96
THR
96
D
LEU
97
n
97
LEU
97
D
ASN
98
n
98
ASN
98
D
PHE
99
n
99
PHE
99
D
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
4970
-42
8740
5030
-39
8740
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
3
A
N
ILE
3
B
O
LEU
97
B
O
LEU
97
B
N
ASN
98
B
N
ASN
98
A
O
THR
96
A
O
THR
96
A
O
ILE
15
A
O
ILE
15
A
N
GLN
18
A
N
GLN
18
A
O
LEU
23
A
O
LEU
23
A
N
ILE
85
A
N
ILE
85
A
N
ILE
84
A
N
ILE
84
A
O
VAL
32
A
O
VAL
32
A
N
LEU
33
A
N
LEU
33
A
O
LEU
76
A
O
LEU
76
A
O
VAL
77
A
O
VAL
77
A
N
ARG
57
A
N
ARG
57
A
N
GLN
58
A
N
GLN
58
A
O
LYS
43
A
O
LYS
43
A
N
GLY
49
A
N
GLY
49
A
O
GLY
52
A
O
GLY
52
A
N
GLU
65
A
N
GLU
65
A
O
ARG
14
A
O
ARG
14
B
O
ILE
47
B
O
ILE
47
B
N
ILE
54
B
N
ILE
54
B
N
GLU
65
B
N
GLU
65
B
O
ARG
14
B
O
ARG
14
B
O
ILE
15
B
O
ILE
15
B
N
GLN
18
B
N
GLN
18
B
O
LEU
23
B
O
LEU
23
B
N
ILE
85
B
N
ILE
85
B
N
ILE
84
B
N
ILE
84
B
O
VAL
32
B
O
VAL
32
B
N
THR
31
B
N
THR
31
B
O
THR
74
B
O
THR
74
B
N
VAL
77
B
N
VAL
77
B
O
ARG
57
B
O
ARG
57
C
O
ILE
47
C
O
ILE
47
C
N
ILE
54
C
N
ILE
54
C
N
GLU
65
C
N
GLU
65
C
O
ARG
14
C
O
ARG
14
C
N
ILE
15
C
N
ILE
15
C
O
GLN
18
C
O
GLN
18
C
O
LEU
23
C
O
LEU
23
C
N
ILE
85
C
N
ILE
85
C
N
ILE
84
C
N
ILE
84
C
O
VAL
32
C
O
VAL
32
C
N
THR
31
C
N
THR
31
C
O
THR
74
C
O
THR
74
C
N
VAL
77
C
N
VAL
77
C
O
ARG
57
C
O
ARG
57
D
N
ASN
98
D
N
ASN
98
C
O
THR
96
C
O
THR
96
C
O
LEU
97
C
O
LEU
97
D
N
ILE
3
D
N
ILE
3
D
N
GLY
49
D
N
GLY
49
D
O
GLY
52
D
O
GLY
52
D
N
GLU
65
D
N
GLU
65
D
O
ARG
14
D
O
ARG
14
D
O
ILE
15
D
O
ILE
15
D
N
GLN
18
D
N
GLN
18
D
O
LEU
23
D
O
LEU
23
D
N
ILE
85
D
N
ILE
85
D
N
ILE
84
D
N
ILE
84
D
O
VAL
32
D
O
VAL
32
D
N
LEU
33
D
N
LEU
33
D
O
LEU
76
D
O
LEU
76
D
O
VAL
77
D
O
VAL
77
D
N
ARG
57
D
N
ARG
57
1
A
CG1
ILE
3
A
CG1
ILE
3
1
Y
1
A
CG2
ILE
3
A
CG2
ILE
3
1
Y
1
A
CD1
ILE
3
A
CD1
ILE
3
1
Y
1
A
CG
ARG
14
A
CG
ARG
14
1
Y
1
A
CD
ARG
14
A
CD
ARG
14
1
Y
1
A
NE
ARG
14
A
NE
ARG
14
1
Y
1
A
CZ
ARG
14
A
CZ
ARG
14
1
Y
1
A
NH1
ARG
14
A
NH1
ARG
14
1
Y
1
A
NH2
ARG
14
A
NH2
ARG
14
1
Y
1
A
CG
GLN
18
A
CG
GLN
18
1
Y
1
A
CD
GLN
18
A
CD
GLN
18
1
Y
1
A
OE1
GLN
18
A
OE1
GLN
18
1
Y
1
A
NE2
GLN
18
A
NE2
GLN
18
1
Y
1
A
CG
LEU
19
A
CG
LEU
19
1
Y
1
A
CD1
LEU
19
A
CD1
LEU
19
1
Y
1
A
CD2
LEU
19
A
CD2
LEU
19
1
Y
1
A
CG
LYS
41
A
CG
LYS
41
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
LYS
43
A
CG
LYS
43
1
Y
1
A
CD
LYS
43
A
CD
LYS
43
1
Y
1
A
CE
LYS
43
A
CE
LYS
43
1
Y
1
A
NZ
LYS
43
A
NZ
LYS
43
1
Y
1
A
CG
GLU
65
A
CG
GLU
65
1
Y
1
A
CD
GLU
65
A
CD
GLU
65
1
Y
1
A
OE1
GLU
65
A
OE1
GLU
65
1
Y
1
A
OE2
GLU
65
A
OE2
GLU
65
1
Y
1
A
CG
LYS
70
A
CG
LYS
70
1
Y
1
A
CD
LYS
70
A
CD
LYS
70
1
Y
1
A
CE
LYS
70
A
CE
LYS
70
1
Y
1
A
NZ
LYS
70
A
NZ
LYS
70
1
Y
1
A
CG
GLN
92
A
CG
GLN
92
1
Y
1
A
CD
GLN
92
A
CD
GLN
92
1
Y
1
A
OE1
GLN
92
A
OE1
GLN
92
1
Y
1
A
NE2
GLN
92
A
NE2
GLN
92
1
Y
1
B
CG
GLN
2
B
CG
GLN
2
1
Y
1
B
CD
GLN
2
B
CD
GLN
2
1
Y
1
B
OE1
GLN
2
B
OE1
GLN
2
1
Y
1
B
NE2
GLN
2
B
NE2
GLN
2
1
Y
1
B
CG
LYS
7
B
CG
LYS
7
1
Y
1
B
CD
LYS
7
B
CD
LYS
7
1
Y
1
B
CE
LYS
7
B
CE
LYS
7
1
Y
1
B
NZ
LYS
7
B
NZ
LYS
7
1
Y
1
B
CG
ARG
14
B
CG
ARG
14
1
Y
1
B
CD
ARG
14
B
CD
ARG
14
1
Y
1
B
NE
ARG
14
B
NE
ARG
14
1
Y
1
B
CZ
ARG
14
B
CZ
ARG
14
1
Y
1
B
NH1
ARG
14
B
NH1
ARG
14
1
Y
1
B
NH2
ARG
14
B
NH2
ARG
14
1
Y
1
B
CG
GLN
18
B
CG
GLN
18
1
Y
1
B
CD
GLN
18
B
CD
GLN
18
1
Y
1
B
OE1
GLN
18
B
OE1
GLN
18
1
Y
1
B
NE2
GLN
18
B
NE2
GLN
18
1
Y
1
B
CG
LEU
19
B
CG
LEU
19
1
Y
1
B
CD1
LEU
19
B
CD1
LEU
19
1
Y
1
B
CD2
LEU
19
B
CD2
LEU
19
1
Y
1
B
CG
MET
36
B
CG
MET
36
1
Y
1
B
SD
MET
36
B
SD
MET
36
1
Y
1
B
CE
MET
36
B
CE
MET
36
1
Y
1
B
CG
ASN
37
B
CG
ASN
37
1
Y
1
B
OD1
ASN
37
B
OD1
ASN
37
1
Y
1
B
ND2
ASN
37
B
ND2
ASN
37
1
Y
1
B
CG
LYS
41
B
CG
LYS
41
1
Y
1
B
CD
LYS
41
B
CD
LYS
41
1
Y
1
B
CE
LYS
41
B
CE
LYS
41
1
Y
1
B
NZ
LYS
41
B
NZ
LYS
41
1
Y
1
B
CG
LYS
43
B
CG
LYS
43
1
Y
1
B
CD
LYS
43
B
CD
LYS
43
1
Y
1
B
CE
LYS
43
B
CE
LYS
43
1
Y
1
B
NZ
LYS
43
B
NZ
LYS
43
1
Y
1
B
CG
LYS
45
B
CG
LYS
45
1
Y
1
B
CD
LYS
45
B
CD
LYS
45
1
Y
1
B
CE
LYS
45
B
CE
LYS
45
1
Y
1
B
NZ
LYS
45
B
NZ
LYS
45
1
Y
1
B
CG
GLN
61
B
CG
GLN
61
1
Y
1
B
CD
GLN
61
B
CD
GLN
61
1
Y
1
B
OE1
GLN
61
B
OE1
GLN
61
1
Y
1
B
NE2
GLN
61
B
NE2
GLN
61
1
Y
1
B
CG
LYS
70
B
CG
LYS
70
1
Y
1
B
CD
LYS
70
B
CD
LYS
70
1
Y
1
B
CE
LYS
70
B
CE
LYS
70
1
Y
1
B
NZ
LYS
70
B
NZ
LYS
70
1
Y
1
B
CG
ARG
87
B
CG
ARG
87
1
Y
1
B
CD
ARG
87
B
CD
ARG
87
1
Y
1
B
NE
ARG
87
B
NE
ARG
87
1
Y
1
B
CZ
ARG
87
B
CZ
ARG
87
1
Y
1
B
NH1
ARG
87
B
NH1
ARG
87
1
Y
1
B
NH2
ARG
87
B
NH2
ARG
87
1
Y
1
C
CG
GLN
2
C
CG
GLN
2
1
Y
1
C
CD
GLN
2
C
CD
GLN
2
1
Y
1
C
OE1
GLN
2
C
OE1
GLN
2
1
Y
1
C
NE2
GLN
2
C
NE2
GLN
2
1
Y
1
C
CG1
ILE
3
C
CG1
ILE
3
1
Y
1
C
CG2
ILE
3
C
CG2
ILE
3
1
Y
1
C
CD1
ILE
3
C
CD1
ILE
3
1
Y
1
C
CG
LYS
7
C
CG
LYS
7
1
Y
1
C
CD
LYS
7
C
CD
LYS
7
1
Y
1
C
CE
LYS
7
C
CE
LYS
7
1
Y
1
C
NZ
LYS
7
C
NZ
LYS
7
1
Y
1
C
CG
ARG
14
C
CG
ARG
14
1
Y
1
C
CD
ARG
14
C
CD
ARG
14
1
Y
1
C
NE
ARG
14
C
NE
ARG
14
1
Y
1
C
CZ
ARG
14
C
CZ
ARG
14
1
Y
1
C
NH1
ARG
14
C
NH1
ARG
14
1
Y
1
C
NH2
ARG
14
C
NH2
ARG
14
1
Y
1
C
CG1
ILE
15
C
CG1
ILE
15
1
Y
1
C
CG2
ILE
15
C
CG2
ILE
15
1
Y
1
C
CD1
ILE
15
C
CD1
ILE
15
1
Y
1
C
CG
LEU
19
C
CG
LEU
19
1
Y
1
C
CD1
LEU
19
C
CD1
LEU
19
1
Y
1
C
CD2
LEU
19
C
CD2
LEU
19
1
Y
1
C
CG
ASN
37
C
CG
ASN
37
1
Y
1
C
OD1
ASN
37
C
OD1
ASN
37
1
Y
1
C
ND2
ASN
37
C
ND2
ASN
37
1
Y
1
C
CG
LYS
41
C
CG
LYS
41
1
Y
1
C
CD
LYS
41
C
CD
LYS
41
1
Y
1
C
CE
LYS
41
C
CE
LYS
41
1
Y
1
C
NZ
LYS
41
C
NZ
LYS
41
1
Y
1
C
CG
LYS
43
C
CG
LYS
43
1
Y
1
C
CD
LYS
43
C
CD
LYS
43
1
Y
1
C
CE
LYS
43
C
CE
LYS
43
1
Y
1
C
NZ
LYS
43
C
NZ
LYS
43
1
Y
1
C
CG
LYS
45
C
CG
LYS
45
1
Y
1
C
CD
LYS
45
C
CD
LYS
45
1
Y
1
C
CE
LYS
45
C
CE
LYS
45
1
Y
1
C
NZ
LYS
45
C
NZ
LYS
45
1
Y
1
C
CG
LYS
55
C
CG
LYS
55
1
Y
1
C
CD
LYS
55
C
CD
LYS
55
1
Y
1
C
CE
LYS
55
C
CE
LYS
55
1
Y
1
C
NZ
LYS
55
C
NZ
LYS
55
1
Y
1
C
CG
GLN
61
C
CG
GLN
61
1
Y
1
C
CD
GLN
61
C
CD
GLN
61
1
Y
1
C
OE1
GLN
61
C
OE1
GLN
61
1
Y
1
C
NE2
GLN
61
C
NE2
GLN
61
1
Y
1
C
CG
LYS
70
C
CG
LYS
70
1
Y
1
C
CD
LYS
70
C
CD
LYS
70
1
Y
1
C
CE
LYS
70
C
CE
LYS
70
1
Y
1
C
NZ
LYS
70
C
NZ
LYS
70
1
Y
1
D
CG
ARG
14
D
CG
ARG
14
1
Y
1
D
CD
ARG
14
D
CD
ARG
14
1
Y
1
D
NE
ARG
14
D
NE
ARG
14
1
Y
1
D
CZ
ARG
14
D
CZ
ARG
14
1
Y
1
D
NH1
ARG
14
D
NH1
ARG
14
1
Y
1
D
NH2
ARG
14
D
NH2
ARG
14
1
Y
1
D
CG
GLU
34
D
CG
GLU
34
1
Y
1
D
CD
GLU
34
D
CD
GLU
34
1
Y
1
D
OE1
GLU
34
D
OE1
GLU
34
1
Y
1
D
OE2
GLU
34
D
OE2
GLU
34
1
Y
1
D
CG
GLU
35
D
CG
GLU
35
1
Y
1
D
CD
GLU
35
D
CD
GLU
35
1
Y
1
D
OE1
GLU
35
D
OE1
GLU
35
1
Y
1
D
OE2
GLU
35
D
OE2
GLU
35
1
Y
1
D
CG
LYS
41
D
CG
LYS
41
1
Y
1
D
CD
LYS
41
D
CD
LYS
41
1
Y
1
D
CE
LYS
41
D
CE
LYS
41
1
Y
1
D
NZ
LYS
41
D
NZ
LYS
41
1
Y
1
D
CG
LYS
43
D
CG
LYS
43
1
Y
1
D
CD
LYS
43
D
CD
LYS
43
1
Y
1
D
CE
LYS
43
D
CE
LYS
43
1
Y
1
D
NZ
LYS
43
D
NZ
LYS
43
1
Y
1
D
CG
LYS
45
D
CG
LYS
45
1
Y
1
D
CD
LYS
45
D
CD
LYS
45
1
Y
1
D
CE
LYS
45
D
CE
LYS
45
1
Y
1
D
NZ
LYS
45
D
NZ
LYS
45
1
Y
1
D
CG
LYS
55
D
CG
LYS
55
1
Y
1
D
CD
LYS
55
D
CD
LYS
55
1
Y
1
D
CE
LYS
55
D
CE
LYS
55
1
Y
1
D
NZ
LYS
55
D
NZ
LYS
55
1
Y
1
D
CG
GLU
65
D
CG
GLU
65
1
Y
1
D
CD
GLU
65
D
CD
GLU
65
1
Y
1
D
OE1
GLU
65
D
OE1
GLU
65
1
Y
1
D
OE2
GLU
65
D
OE2
GLU
65
1
Y
1
D
CG1
ILE
66
D
CG1
ILE
66
1
Y
1
D
CG2
ILE
66
D
CG2
ILE
66
1
Y
1
D
CD1
ILE
66
D
CD1
ILE
66
1
Y
1
D
CG
LYS
70
D
CG
LYS
70
1
Y
1
D
CD
LYS
70
D
CD
LYS
70
1
Y
1
D
CE
LYS
70
D
CE
LYS
70
1
Y
1
D
NZ
LYS
70
D
NZ
LYS
70
1
Y
1
B
B
O
OD1
ASP
ASN
29
88
2.10
1
C
C
O
OD1
ASP
ASN
29
88
2.13
1
A
GLU
35
-27.27
123.91
1
A
TRP
42
-175.38
136.18
1
A
CYS
67
58.61
70.25
1
B
MET
36
-179.14
121.63
1
B
PRO
79
-63.93
80.12
1
C
GLN
2
-146.52
38.83
1
D
GLU
35
-36.75
159.80
1
D
MET
36
-177.18
-138.58
1
D
TRP
42
-172.24
148.01
1
D
PRO
79
-58.70
30.02
NCS RESTRAINTS IMPOSED BETWEEN THE DIMERS (BUT NOT WITHIN THE DIMERS) TO IMPROVE OBSERVABLES TO PARAMETER RATIO.
0.284
0.223
0.223
2.2
50
1085
13097
13097
71.2
random
1
restrained
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
1F7A
Engh & Huber
2.2
50
28
2972
100
0
2844
0.008
1.4
28.8
1.15
0.37
0.32
2.28
1183
66
2.2
50
1N49
13097
13097
0
0
0.064
1
7.6
71.2
0.27
2.2
2.28
1
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Viability of a Drug-Resistant HIV-1 Protease Variant: Structural Insights for Better Anti-Viral Therapy
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
B
GLY
86
B
GLY
86
HELX_P
B
ILE
93
B
ILE
93
1
2
8
C
GLY
86
C
GLY
86
HELX_P
C
ILE
93
C
ILE
93
1
3
8
D
GLY
86
D
GLY
86
HELX_P
D
ILE
93
D
ILE
93
1
4
8
HYDROLASE/HYDROLASE INHIBITOR
HIV-1 protease, drug resistance, substrate recognition, inhibitor binding, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex
POL_HV1A2
UNP
1
57
P03369
PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
57
155
1N49
1
99
P03369
A
1
1
99
57
155
1N49
1
99
P03369
B
1
1
99
57
155
1N49
1
99
P03369
C
1
1
99
57
155
1N49
1
99
P03369
D
1
1
99
1
GLN
engineered mutation
LYS
7
1N49
A
P03369
UNP
63
7
1
ASP
engineered mutation
ASN
25
1N49
A
P03369
UNP
81
25
1
VAL
engineered mutation
ALA
82
1N49
A
P03369
UNP
138
82
2
GLN
engineered mutation
LYS
7
1N49
B
P03369
UNP
63
7
2
ASP
engineered mutation
ASN
25
1N49
B
P03369
UNP
81
25
2
VAL
engineered mutation
ALA
82
1N49
B
P03369
UNP
138
82
3
GLN
engineered mutation
LYS
7
1N49
C
P03369
UNP
63
7
3
ASP
engineered mutation
ASN
25
1N49
C
P03369
UNP
81
25
3
VAL
engineered mutation
ALA
82
1N49
C
P03369
UNP
138
82
4
GLN
engineered mutation
LYS
7
1N49
D
P03369
UNP
63
7
4
ASP
engineered mutation
ASN
25
1N49
D
P03369
UNP
81
25
4
VAL
engineered mutation
ALA
82
1N49
D
P03369
UNP
138
82
3
9
8
8
3
8
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
B
THR
96
B
THR
96
B
ASN
98
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
VAL
32
A
VAL
32
A
GLU
34
A
GLU
34
A
LYS
70
A
LYS
70
A
GLY
78
A
GLY
78
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
B
LYS
43
B
LYS
43
B
GLY
48
B
GLY
48
B
PHE
53
B
PHE
53
B
ILE
66
B
ILE
66
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLN
18
B
GLN
18
B
LEU
24
B
LEU
24
B
ILE
84
B
ILE
84
B
ILE
85
B
ILE
85
B
THR
31
B
THR
31
B
LEU
33
B
LEU
33
B
ILE
72
B
ILE
72
B
VAL
77
B
VAL
77
B
PHE
53
B
PHE
53
B
ILE
66
B
ILE
66
C
LYS
43
C
LYS
43
C
GLY
48
C
GLY
48
C
PHE
53
C
PHE
53
C
ILE
66
C
ILE
66
C
LEU
10
C
LEU
10
C
ILE
15
C
ILE
15
C
GLN
18
C
GLN
18
C
LEU
24
C
LEU
24
C
ILE
84
C
ILE
84
C
ILE
85
C
ILE
85
C
THR
31
C
THR
31
C
GLU
34
C
GLU
34
C
HIS
69
C
HIS
69
C
GLY
78
C
GLY
78
C
PHE
53
C
PHE
53
C
ILE
66
C
ILE
66
D
THR
96
D
THR
96
D
ASN
98
D
ASN
98
C
THR
96
C
THR
96
C
ASN
98
C
ASN
98
D
GLN
2
D
GLN
2
D
ILE
3
D
ILE
3
D
LYS
43
D
LYS
43
D
GLY
49
D
GLY
49
D
GLY
52
D
GLY
52
D
ILE
66
D
ILE
66
D
LEU
10
D
LEU
10
D
ILE
15
D
ILE
15
D
GLN
18
D
GLN
18
D
LEU
24
D
LEU
24
D
ILE
84
D
ILE
84
D
ILE
85
D
ILE
85
D
VAL
32
D
VAL
32
D
GLU
34
D
GLU
34
D
LYS
70
D
LYS
70
D
GLY
78
D
GLY
78
D
GLY
52
D
GLY
52
D
ILE
66
D
ILE
66
BINDING SITE FOR RESIDUE RIT B 301
B
RIT
301
Software
19
BINDING SITE FOR RESIDUE RIT D 401
D
RIT
401
Software
21
A
ASN
25
A
ASN
25
19
1_555
A
GLY
27
A
GLY
27
19
1_555
A
ALA
28
A
ALA
28
19
1_555
A
ASP
29
A
ASP
29
19
1_555
A
GLY
48
A
GLY
48
19
1_555
A
GLY
49
A
GLY
49
19
1_555
A
ILE
50
A
ILE
50
19
1_555
A
PRO
81
A
PRO
81
19
1_555
A
ILE
84
A
ILE
84
19
1_555
A
HOH
105
G
HOH
19
1_555
B
ARG
8
B
ARG
8
19
1_555
B
ASN
25
B
ASN
25
19
1_555
B
GLY
27
B
GLY
27
19
1_555
B
ASP
30
B
ASP
30
19
1_555
B
VAL
32
B
VAL
32
19
1_555
B
GLY
49
B
GLY
49
19
1_555
B
PRO
81
B
PRO
81
19
1_555
B
ILE
84
B
ILE
84
19
1_555
B
HOH
303
H
HOH
19
1_555
C
ARG
8
C
ARG
8
21
1_555
C
ASN
25
C
ASN
25
21
1_555
C
GLY
27
C
GLY
27
21
1_555
C
ASP
30
C
ASP
30
21
1_555
C
VAL
32
C
VAL
32
21
1_555
C
ILE
47
C
ILE
47
21
1_555
C
GLY
49
C
GLY
49
21
1_555
C
ILE
50
C
ILE
50
21
1_555
C
PRO
81
C
PRO
81
21
1_555
C
ILE
84
C
ILE
84
21
1_555
D
ASN
25
D
ASN
25
21
1_555
D
GLY
27
D
GLY
27
21
1_555
D
ALA
28
D
ALA
28
21
1_555
D
ASP
29
D
ASP
29
21
1_555
D
GLY
48
D
GLY
48
21
1_555
D
GLY
49
D
GLY
49
21
1_555
D
ILE
50
D
ILE
50
21
1_555
D
PRO
81
D
PRO
81
21
1_555
D
ILE
84
D
ILE
84
21
1_555
D
HOH
402
J
HOH
21
1_555
D
HOH
403
J
HOH
21
1_555
4
P 1 21 1